Programmed chromosome fission and fusion enable precise large-scale genome rearrangement and assembly

The design and creation of synthetic genomes provide a powerful approach to understanding and engineering biology. However, it is often limited by the paucity of methods for precise genome manipulation. Here, we demonstrate the programmed fission of the Escherichia coli genome into diverse pairs of synthetic chromosomes and the programmed fusion of synthetic chromosomes to generate genomes with user-defined inversions and translocations. We further combine genome fission, chromosome transplant, and chromosome fusion to assemble genomic regions from different strains into a single genome. Thus, we program the scarless assembly of new genomes with nucleotide precision, a key step in the convergent synthesis of genomes from diverse progenitors. This work provides a set of precise, rapid, large-scale (megabase) genome-engineering operations for creating diverse synthetic genomes.

Reconstruction of evolutionary trajectories of coffee chromosomes

Background Polyploidization is a widespread phenomenon in plants, especially in angiosperms. Because of the rearrangement of chromosomes and the loss of genes, the number of plant chromosomes will reduce. Studies have shown that core dicotyledons are derived from ancestors with seven proto-chromosomes, which triplicated in a core-eudicot-common hexaploidization. Therefore, dicotyledon with different chromosome numbers have evolved on the basis of 21 chromosomes. On this basis, we selected grape as the intermediate reference species to infer the karyotype evolutionary process of coffee. Results We found that all the chromosome fusion forms in grape were end-end joining, and 7 (70.0%) chromosome fusion forms in coffee were end-end joining. In the process of grape forming 19 chromosomes, there were three chromosome fusions and one chromosome fission. In the process of coffee 11 chromosomes formation, 10 chromosome fusions occurred. During the process, we inferred that satellite chromosomes formed by telomeres from the same or different chromosomes were produced; and the lost of them resulted in chromosome number reduction Conclusions Notably, we found that the major fusion mode of chromosomes in coffee is end-end joining, which is well explained by telomere-centric model, shared by grape and possibly by many other eudicots. This is contrastively different from the observation of monocot plants like grasses, in which nested chromosome fusions often occurred. The present work will help to understand the structural and functional innovations of plant chromosomes.

Karyotypic diversification and its contribution to the taxonomy of Eleocharis (Cyperaceae) from Brazil

A karyotype analysis of 147 populations of 25 Brazilian species of Eleocharis (Cyperaceae) was carried out, including representatives of the three subgenera that occur in the country: Limnochloa, Scirpidium and Eleocharis. The analyses showed chromosomes without centromeres, but with terminal nucleolar constrictions (satellites) in some chromosomes. The chromosome numbers varied from 2n = 6 in E. subarticulata and E. maculosa to 2n = 60 in E. laeviglumis, but the chromosome basic number x = 5 was confirmed. Species of the subgenera Eleocharis and Scirpidium possess fewer and larger chromosomes, while those in the subgenus Limnochloa have small and more numerous chromosomes. These features indicate that the karyotypes of the subgenera Eleocharis and Scirpidium are more closely related, in agreement with morphological and phylogenetical data. The representatives of the section Eleocharis exhibited the largest differences in chromosome number and size, probably due to chromosome fission and fusion. Polyploidy was the most common event in this group. Nevertheless, most of the studied species exhibited regular meiosis with only bivalent formation, even the polyploids, such as in E. geniculata and E. sellowiana. The cytogenetic information obtained showed quite variable karyotypes with chromosomes gradually decreasing in size, and predominance of polyploidy. These results are useful in the differentiation of the subgenera.